Interesting that. My Ginb stock has the same arrangement, bolt and trigger guard wise and NM mentioned to me that he knew of one instance where putting the action back in a standard stock cured the problem. The holes for the front bolts on the Ginb are also misaligned as apparently many are. I've tried shimming the metal yoke to compensate but this, as Paul L (Platitude on here) as pointed out, is not a good solution as it puts another stress into the system. He has suggested just fixing the one bolt (temporarily) that is correctly aligned and seeing in there's any difference. Another mate has also loaned me a stock that mounts with the two bolts through the trigger guard to try so we're on a similar track there.
I would like to agree with you but then we'd both be wrong....